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Biochemical and genetic characterization of the tet determinant of Bacillus plasmid pAB124.

A fragment of Bacillus plasmid pAB124 carrying the genes encoding tetracycline resistance was previously cloned into Escherichia coli plasmid pSF2124 (S.J. Eccles, A. Docherty, I. Chopra, S. Shales, and P. Ball, J. Bacteriol. 145:1417-1420, 1981). The cloned pAB124 tet fragment conferred low-level resistance in E. coli, but exposure of this strain to a subinhibitory level of tetracycline led to selection of a mutant plasmid in which high-level resistance, associated with decreased drug accumulation, was expressed constitutively. In this plasmid, the Bacillus tet determinant appeared to be transcribed from a promoter on the vector. Construction of tetracycline-sensitive derivatives of this plasmid by transposon insertion mutagenesis allowed identification of a 32,000-dalton membrane-located protein, which apparently promoted decreased accumulation of tetracycline. This protein was also synthesized as a 32,000-dalton polypeptide in a coupled, in vitro transcription-translation system directed by plasmid DNA. The pAB124 tet determinant differed from the tetA through tetD determinants found in gram-negative bacteria in DNA-DNA hybridization and in the ability to prevent accumulation of different tetracycline derivatives, but was closely related to the tet determinant of another plasmid isolated from Bacillus species, pBC16.

Bacillus subtilis↗

Repressor gene finO in plasmids R100 and F: constitutive transfer of plasmid F is caused by insertion of IS3 into F finO.

Fertility factor F confers bacterial conjugation, a process which involves at least 20 tra genes. Resistance plasmids such as R100, R6-5, and R1 have homology with F in the tra region. Conjugal transfer of these plasmids is, however, repressed, while transfer of F is constitutive. Repression of R transfer is due to the existence of the two genes, called finO and finP; constitutive transfer of F is believed to be due to a lack of finO in F. In this paper, we report the identification and DNA sequence of the finO gene of R100, encoding a protein of 21,265 daltons. We show that F does actually encode finO, but the gene has been inactivated by insertion of IS3. Lederberg and Tatum (Nature [London] 158:558, 1946), who discovered sexuality in bacteria, may have had an Escherichia coli K-12 strain harboring such an finO F factor, which facilitated the generation of recombinant progeny useful for genetic analysis of bacteria and established the foundation for molecular genetics.

Amino Acid Sequence↗

Four frameshift mutations in neurofibromatosis type 1 caused by small insertions.

We have been using heteroduplex analysis to assay individual exons within the NF1 gene in an effort to identify disease causing constitutional mutations in neurofibromatosis type 1 patients. Here we report the identification and characterisation of four insertional NF1 frameshift mutations in an analysis of exons 28-39 in a set of 78 patients. These include three 1 base pair insertions and one 2 base pair insertion. Three of these mutations can be attributed to replication slippage errors, while the mechanism behind the fourth may be related to formation of secondary structure during replication. It may be of significance that a majority of the previously reported small insertions in NF1 also lie within exons 28-39.

Adult↗

New Leptospira serovar Sokoine of serogroup Icterohaemorrhagiae from cattle in Tanzania.

The prevalence of leptospirosis is generally high in domestic animals and rodents in Tanzania. Identification of Leptospira isolates from cattle was carried out to establish prevalent Leptospira serovars. Serological typing was done based on monoclonal antibodies and the standard cross-agglutination absorption test. Molecular typing involved pathogenic- and saprophytic-specific PCRs and a PCR specifically amplifying DNA from the species Leptospira kirschneri. DNA fingerprinting with primers derived from sequences of insertion elements IS1500 and IS1533 was carried out. Both serological and molecular characterization indicated that one of the Leptospira isolates, coded RM1, represents a new serovar of the species L. kirschneri of serogroup Icterohaemorrhagiae. The serovar name Sokoine is proposed for this new Leptospira isolate.

Agglutination Tests↗

Proteolytic processing of Ty3 proteins is required for transposition.

Ty3 is a retroviruslike element found in Saccharomyces cerevisiae. It encodes GAG3 and GAG3-POL3 polyproteins which are processed into mature proteins found in the Ty3 viruslike particle. In this study, the region encoding a protease that is homologous to retroviral aspartyl proteases was identified and shown to be required for production of mature Ty3 proteins and transposition. The Ty3 protease has the Asp-Ser-Gly consensus sequence found in copia, Ty1, and Rous sarcoma virus proteases, rather than the Asp-Thr-Gly found in most retroviral proteases. The Asp-Ser-Gly consensus is flanked by residues similar to those which flank the active sites of cellular aspartyl proteases. Mutations were made in the Ty3 active-site sequence to examine the role of the protease in Ty3 particle maturation and to test the functional significance of the Ser active-site variant in the consensus sequence. Mutation of the active-site Asp blocked processing of Gag3 and Gag3-Pol3 and allowed identification of a GAG3-POL3 polyprotein. This protein was turned over rapidly in cells expressing the mutant Ty3. Changing the active-site Ser to Thr caused only a modest reduction in the levels of certain Ty3 proteins. Five putative cleavage sites of this protease in Ty3 GAG3 and GAG3-POL3 polyproteins were defined by amino-terminal sequence analysis. The existence of an additional protein(s) of unknown function, encoded downstream of the protease-coding region, was deduced from the positions of these amino termini and the sizes of known Ty3 proteins. Although Ty3 protease cleavage sites do not correspond exactly to known retroviral protease cleavage sites, there are similarities. Residues P3 through P2' in the regions encompassing each of the five sites are uncharged, and no P1 position is occupied by an amino acid with a branched beta carbon.

Amino Acid Sequence↗

IS1139 from Streptococcus salivarius: identification and characterization of an insertion sequence-like element related to mobile DNA elements from gram-negative bacteria.

An insertion sequence-like element, IS1139, was cloned and sequenced from Streptococcus salivarius ATCC 25975 chromosome. This insertion sequence-like element is 1168 bp long and is delimited by inverted repeats of 29 bp and by a duplicated sequence of 6 bp. This IS possesses an open reading frame that codes for a putative transposase of 339 amino acids which has, respectively, 94, 35, 33, and 30% amino-acid identity with the transposases of IS1161 from S. salivarius ATCC 25975, IS4351 from Bacteroides fragilis, IS30 from Escherichia coli, and IS1086 from Alcaligenes eutrophus. Sequence analysis revealed that these transposases may have evolved from a common ancestral gene. Southern hybridization of restriction endonuclease-digested genomic DNA from 21 strains of oral streptococci, using a probe specific to the transposase-encoding gene (tnpA), revealed that IS1139 is found in two strains of S. salivarius, ATCC 25975 and ATCC 13419, in eight and two copies, respectively.

Alcaligenes↗

Rapid detection and identification of Mycobacterium tuberculosis by Real Time PCR and Bactec 960 MIGT.

We have developed a Real-Time PCR assay to detect M. tuberculosis using the iCycler iQ detection system by TaqMan assay directly on the clinical specimen. A total of 513 clinical samples were taken from patients with suspected tuberculosis and other patients that had an active mycobacterial infection, as well as patients with diagnosed tuberculosis who were receiving antitubercular therapy. The sensitivity and specificity of this assay, 10% and 100%, respectively, were compared to those of conventional microbiological methods.

DNA Transposable Elements↗

Analysis of the yeast SPT3 gene and identification of its product, a positive regulator of Ty transcription.

Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutant phenotypes, including defects in sporulation and diploid formation. In this paper we report further genetic and physical characterization of the SPT3 gene and protein. By extensive linker insertion mutagenesis, we have delimited the region necessary for SPT3 function. From DNA sequence analysis, SPT3 encodes a protein of 337 amino acids. We have identified this protein with an anti-SPT3 antibody. Finally, we show that overproduction of the SPT3 gene product does not alter the level of Ty transcription.

Amino Acid Sequence↗

Repetitive nucleotide sequence insertions into a novel calmodulin-related gene and its processed pseudogene.

A gene containing a transposon-like human repeat element, called THE 1, has been isolated and characterized. The gene, termed T+, encodes a polypeptide resembling known calcium-binding proteins. The THE 1 element is present in the 3'-untranslated region of its message. The cDNA clone corresponding to the gene's mRNA product led to the identification of this gene. A processed RNA pseudogene related to the authentic gene has also been isolated. In addition to intron processing, this pseudogene differs from the gene in that it contains an interspersed Alu repeat instead of a THE 1 element in the 3'-untranslated region. Thus, we compare a site containing a THE 1 element to an ancestrally related transposon-less target site. The comparison suggests a retroviral-related mechanism of THE 1 insertion. This system is unusual in that the parent gene is associated with three distinct retrotransposition events: the parent gene was converted to a processed RNA pseudogene, an Alu repeat inserted into the pseudogene, and a THE 1 element inserted into the parent gene.

Amino Acid Sequence↗

Identification of transposon insertion mutants of Francisella tularensis tularensis strain Schu S4 deficient in intracellular replication in the hepatic cell line HepG2.

BACKGROUND: Francisella tularensis is a zoonotic intracellular bacterial pathogen that causes tularemia. The subspecies tularensis is highly virulent and is classified as a category A agent of biological warfare because of its low infectious dose by an aerosol route, and its ability to cause severe disease. In macrophages F. tularensis exhibits a rather novel intracellular lifestyle; after invasion it remains in a phagosome for three to six hours before escaping to, and replicating in the cytoplasm. The molecular mechanisms that allow F. tularensis to invade and replicate within a host cell have not been well defined. METHODS: We constructed a stable transposon mutagenesis library of virulent strain Schu S4 using a derivative of the EZ::TN transposon system. Approximately 2000 mutants were screened for the inability to invade, and replicate in the hepatic carcinoma cell line HepG2. These mutants were also tested for replication within the J774.1 macrophage-like cell line. RESULTS: Eighteen mutants defective in intracellular replication in HepG2 cells were identified. Eight of these mutants were auxotrophs; seven had mutations in nucleotide biosynthesis pathways. The remaining mutants had insertions in genes that were predicted to encode putative transporters, enzymes involved in protein modification and turnover, and hypothetical proteins. A time course of the intracellular growth of a pyrB mutant revealed that this mutant was only able to grow at low levels within HepG2 cells but grew like wild-type bacteria in J774.1 cells. This pyrB mutant was also attenuated in mice. CONCLUSION: This is the first reported large-scale mutagenesis of a type A strain of F. tularensis and the first identification of mutants specifically defective in intracellular growth in a hepatic cell line. We have identified several genes and pathways that are key for the survival and growth of F. tularensis in a hepatic cell line, and a number of novel intracellular growth-defective mutants that have not been previously characterized in other pathogens. Further characterization of these mutants will help provide a better understanding of the pathogenicity of F. tularensis, and may have practical applications as targets for drugs or attenuated vaccines.

Animals↗

[Construction of mutant population of differential race of Xa23 resistant to rice bacterial blight and avirulence activity identification of mutants].

The mutant population of Xanthomonas oryzae pv oryzae strain differential to rice bacterial blight resistance gene Xa23 has been constructed mediated by transposon in vivo . The results of PCR amplification with specific primers and analysis of flanking sequence of mutants indicated that the foreign DNA has been integrated into X. oryzae pv oryzae genome. Four mutants with changed avirulent activity to Xa23 gene have been identified by artificial inoculation. It is possible to clone genes that are required for AvrXa23 avirulence activity using this new strategy.

Bacterial Proteins↗

Identification of an IS6110 insertion site in plcD, the unique phospholipase C gene of Mycobacterium bovis.

The IS6110 repetitive element is present in multiple copies in most Mycobacterium tuberculosis complex bacteria, except for Mycobacterium bovis strains, which usually contain a single copy of IS6110 located on a 1.9 kb PvuII fragment of the direct repeat region. IS6110 transposition can disrupt coding regions and is a major force of genomic variation. In a previous work it was demonstrated that phospholipase C genes are preferential loci for IS6110 transposition in M. tuberculosis clinical strains. Bacterial phospholipase C enzymes participate in pathogenic mechanisms used by different organisms, and have been implicated in intracellular survival, cytolysis and cell-to-cell spread. Four phospholipase C genes (plcA, plcB, plcC and plcD) were detected in the genomes of M. tuberculosis, Mycobacterium africanum, Mycobacterium microti and 'Mycobacterium canettii'. M. bovis and the vaccine strain M. bovis Bacillus Calmette-Guérin contain only the plcD gene. In the present work, the existence of IS6110 insertions within plcD, the unique phospholipase C gene of M. bovis, has been investigated by PCR, Southern blot hybridization and sequencing analysis. In 18 (7.3 %) of 245 isolates analysed, the plcD gene was interrupted by the insertion of one copy of IS6110, which in all cases was transposed in the same orientation and at the same position, 1 972 894, relative to the genome of M. bovis AF2122/97. These 18 isolates were distributed in 6 different spoligotype patterns and contained 4 to 8 IS6110 copies. In contrast, strains showing an intact plcD gene contained one (87 %), two (9.4 %) or three (2.4 %) IS6110 copies, and only a single isolate (1.2 %) had four IS6110 copies. The implications of plcD gene disruption in M. bovis have not been fully investigated, but no differences in the organ distribution of the disease were detected when animals infected with strains from the same spoligotype patterns bearing plcD : : IS6110 and intact plcD were compared.

DNA Fingerprinting↗

Resolution of a hybrid cointegrate between transposons Tn501 and Tn1721 defines the recombination site.

The related transposons Tn501 and Tn1721 have a 3.8 kb region in common that contains two genes (tnpA and tnpR) and a resolution site (res) required for transposition. Resolvase, the product of tnpR, catalyses site-specific recombination at res, a 186 base pair (bp) sequence located adjacent to tnpR at one end of the homology region. We describe here identification of the crossover site within res. It involved the construction of a plasmid containing copies of res (Tn501) and res (Tn1721) in direct orientation and tnpR-mediated intramolecular recombination between the two homologous (but non-identical) sites. The resulting hybrid contained Tn501 and Tn1721 fused at the crossover point. DNA sequence analysis of the recombinant indicates that recombination occurs in an 11 bp region of exact homology between Tn501 and Tn1721. The recombination site lies 161-172 bp upstream of tnpR at the transition from homology to non-homology between Tn501 and Tn1721 suggesting that site-specific recombination may have played a role in the evolution of these elements.

Base Sequence↗

Identification of an IS711 element interrupting the wboA gene of Brucella abortus vaccine strain RB51 and a PCR assay to distinguish strain RB51 from other Brucella species and strains.

Brucella abortus vaccine strain RB51 is a natural stable attenuated rough mutant derived from the virulent strain 2308. The genetic mutations that are responsible for the roughness and the attenuation of strain RB51 have not been identified until now. Also, except for an assay based on pulsed-field gel electrophoresis, no other simple method to differentiate strain RB51 from its parent strain 2308 is available. In the present study, we demonstrate that the wboA gene encoding a glycosyltransferase, an enzyme essential for the synthesis of O antigen, is disrupted by an IS711 element in B. abortus vaccine strain RB51. Exploiting this feature, we developed a PCR assay that distinguishes strain RB51 from all other Brucella species and strains tested.

Animals↗

Imperfect DNA mirror repeats in E. coli TnsA and other protein-coding DNA.

DNA imperfect mirror repeats (DNA-IMRs) are ubiquitous in protein-coding DNA. However, they overlap and often have different centers of symmetry, making it difficult to evaluate their relationship to each other and to specific DNA and protein motifs and structures. This paper describes a systematic method of determining a hierarchy for DNA-IMRs and evaluates their relationship to protein structural elements (PSEs)--helices, turns and beta-sheets. DNA-IMRs are identifed by two different methods--DNA-IMRs terminated by reverse dinucleotides (rd-IMRs) and DNA-IMRs terminated by a single (mono) matching nucleotide (m-IMRs). Both rd-IMRs and m-IMRs are evaluated in 17 proteins, and illustrated in detail for TnsA. For each of the proteins, Fisher's exact test (FET) is used to measure the coincidence between the terminal dinucleotides of rd-IMRs and the terminal amino acids of individual PSEs. A significant correlation over a span of about 3 nt was found for each protein. The correlation is robust and for most genes, all rd-IMRs 16 nt contain approximately 88% of the potential functional motifs. The protein translation of the longest rd- and m-IMRs span sequences important to the protein's structure and function. In all 17 proteins studied, the population of rd-IMRs is substantially less than the expected number and the population of m-IMRs greater than the expected number, indicating strong selective pressures. The association of rd-IMRs with PSEs restricts their spatial distribution, and therefore, their number. The greater than predicted number of m-IMRs indicates that DNA symmetry exists throughout the entire protein-coding region and may stabilize the sequence.

Amino Acid Sequence↗

Identification of DNA amplifications near the center of the Streptomyces coelicolor M145 chromosome.

Linear streptomycete chromosomes frequently undergo spontaneous gross DNA rearrangements at the terminal regions. Large DNA deletions of the chromosome ends are in many cases associated with tandemly reiterated DNA amplifications, found at the border of the deletable areas. In contrast to previous reports, we have discovered amplifications near the center of the Streptomyces coelicolor M145 chromosome. The detected amplified units of DNA are 19.9 kb and 16 kb in length and exist in copy numbers of 30 and 40, respectively. Both amplifications were located in the same region and share at least 3.6 kb.

Chromosomes, Bacterial↗

Modifiers of muscle and heart cell fate specification identified by gain-of-function screen in Drosophila.

The homeobox genes ladybird in Drosophila and their vertebrate counterparts Lbx1 genes display restricted expression patterns in a subset of muscle precursors and are both implicated in diversification of muscle cell fates. In order to gain new insights into mechanisms controlling conserved aspects of cell fate specification, we have performed a gain-of-function (GOF) screen for modifiers of the mesodermal expression of ladybird genes using a collection of EP element carrying Drosophila lines. Amongst the identified genes, several have been previously implicated in cell fate specification processes, thus validating the strategy of our screen. Observed GOF phenotypes have led us to identification of an important number of candidate genes, whose myogenic and/or cardiogenic functions remain to be investigated. Amongst them, the EP insertions close to rhomboid, yan and rac2 suggest new roles for these genes in diversification of muscle and/or heart cell lineages. The analysis of loss and GOF of rhomboid and yan reveals their new roles in specification of ladybird-expressing precursors of adult muscles (LaPs) and ladybird/tinman-positive pericardial cells. Observed phenotypes strongly suggest that rhomboid and yan act at the level of progenitor and founder cells and contribute to the diversification of mesodermal fates. Our analysis of rac2 phenotypes clearly demonstrates that the altered mesodermal level of Rho-GTPase Rac2 can influence specification of a number of cardiac and muscular cell types including those expressing ladybird. Finding that in rac2 mutants ladybird and even skipped-positive muscle founders are overproduced, indicate a new early function for this gene during segregation of muscle progenitors and/or specification of founder cells. Intriguingly, rhomboid, yan and rac2 act as conserved components of Receptor Tyrosine Kinases (RTKs) signalling pathways, suggesting that RTK signalling constitutes a part of a conserved regulatory network governing diversification of muscle and heart cell types.

Animals↗

IS1394 from Pseudomonas alcaligenes N.C.I.B. 9867: identification and characterization of a member of the IS30 family of insertion elements.

A new insertion sequence designated IS1394 was isolated from Pseudomonas alcaligenes NCIB 9867 (P25X) by entrapment in plasmid pUCD800 which carries the Bacillus subtilis sacB and sacR genes. The 1100-bp sequence contains 27-bp inverted repeats with 4 bp mismatch and has one long open reading frame, spanning 92.1% of the entire IS. The deduced 338 amino-acid sequence demonstrated homology (varying from 65% to 78% similarity and 36-67% identity) to transposases encoded by the IS30 family of IS elements. Comparison of four different IS-sacB junction sequences showed that IS1394 generated 3-bp direct repeats of target DNA upon insertion. IS1394 is present in at least 10 copies in the P25X genome but none was detected in its endogenous plasmid pRA2. Hybridization experiments revealed that the distribution of IS1394 is limited to closely related strains, being present in three copies in Pseudomonas putida NCIB 9869 (P35X) and two copies in Pseudomonas alcaligenes ATCC type strain (ATCC 14904).

Base Sequence↗